Sandbox 46



=Trypsin= Trypsin, a member of the serine protease family, is produced in the pancreas and found in the digestive tracks of vertebrates. To avoid pancreatic self-degradation, trypsin is synthesized as trypsinogen, a zymogen. Cleavage by enteropeptidase allows tryspin to enter its active form. As a serine protease, trypsin contains a serine residue in its active site.

Structure
The trypsin structure displayed is a mutant form isolated from a bovine pancreas. It contains 58 amino acid residues as well as an altered binding loop. To follow the primary structure (amino acid sequence) of Trypsin, click here. Begin at the N-terminus (blue) and move toward the C-terminus (red).

The secondary structure of Trypsin consists of two alpha helices (light green) and two beta sheets (peach). Hydrophobic interactions - mainly the hydrophobic collapse - significantly contribute to both secondary and tertiary structure. This structure shows that the majority of the residues are non-polar/hydrophobic (maroon). These residues tend to congregate on the interior of the structure while polar/hydrophilic residues (blue) remain on the exterior. This orientation allows polar molecules to maximize interaction with water and other polar molecules while non-polar molecules minimize such interactions. Adding water molecules to the model, the polar/non-polar interactions can be seen. The color configuration remains with water molecules displayed in green.

Stability
Many factors contribute to protein stabilization. Disulphide bonds form between the Sulfur atoms of two Cysteine residues and assist in the formation of the tertiary structure. This particular form of trypsin contains three disulphide bonds (yellow). These bonds interact between Cysteine residues at positions 5 and 55, 14 and 38, 30 and 51. Disulphide bond two (residues 14 and 38) interacts with two chiral centers; thus, one Sulfur atom interacts with two Sulfur atoms opposite it. Click here to see the labeled disulphide bonds. In addition to disulphide bonds, Hydrogen bonding plays a large role in stability. As this model suggests, hydrogen bonds (orange) are most prominent in alpha helices and beta sheets of the backbone. In alpha helices, hydrogen bonds form between an H-N and a C-O 4 residues away; complementing the specific turn length (3.6 residues). Hydrogen bonds between the sidechain residues (R groups) provide further stability for the trypsin moiety.

The yellow and red molecules represent SO4 (2-) molecules which are not part of the traditional trypsin structure; they were added during crystallization to freeze Trypsin in a specific conformation. Each SO4 molecule is bound to an active site (ball and stick display) in order to prevent interaction with another substrate. Active site inhibition is a prominent method for studying enzymes.

Function
Enteropeptidase cleaves after Lysine if it is preceded by 4 Aspartic Acid residues and not followed by a Proline residue. This particular cleavage converts trypsinogen (zymogen) into trypsin. Once activated, trypsin catalyzes the hydrolysis of peptides into amino acids which the body can absorb during digestion. Trypsin has an affinity for positively charged molecules; thus, it specifically cleaves on the carboxyl end (after) of Lysine and Arginine, unless Proline follows the residue. Trypsin's active site normally contains a triad of residues: Histidine, Serine, and Apartic Acid. The particular mutant form discussed here does not contain this particular active site, but rather 4 different active sites. Click on any of the following links to view a specific active site: Active Site 1 (light blue); Active Site 2 (pink); Active Site 3 (yellow); Active Site 4 (dark blue). This model compares the orientation of all four active sites. Site 1 and 3 share a small portion (Arginine residue 42) which is shown in maroon. Active site three most closely resembles the traditional composition of trypsin's active site.